%% INTRODUCTION

\newglossaryentry{innate system}{
name={innate system},
description={encompasses \glspl{white blood cell} that identify and neutralize the historically most common invaders by recognizing patterns of molecules characteristic of general categories of \glspl{pathogen}. \emph{See:} section \ref{introduction}},
}
\newglossaryentry{adaptive system}{
name={adaptive system},
description={identifies molecules (usually specific proteins) found only in a specific strain of the \gls{pathogen}. \emph{See:} section \ref{introduction}},
}


%% IMMUNE OVERVIEW

\newdualentry{APC}{antigen presenting cell}{%
antigen presenting cells}{are cells that display foreign antigens in \acrfull{MHC} on their surfaces, for presentation to T cells. \emph{See:} section \ref{apc}.}

\newdualentry{MHC}{major histocompatibility complex}{major histocompatibility complexes}{%
proteins presented in the cell when activated by an antigen. \emph{Related:} section \ref{apc}.}

\newglossaryentry{cytokine}{
name={cytokine},
description={means of immune communication. \emph{See:} section \ref{cytokines}.},
}

\newglossaryentry{neutrophils}{
name={neutrophils},
description={are our body's white blood first line of defense; these cells destroy everything in sight. Fortunately they are also fast lived and quickly regulated by \glspl{thcell}, so they act as a first preempt defensive strike. Pus is mostly made of neutrophils.},
plural={neutrophils},
}
\newglossaryentry{macrophage}{
name={macrophage},
description={are ``sentinel'' cells that lack mobility. Their main function is in cleaning up debris in the blood, phagocyting debris as garbage collectors. But they may be recruited for infection fighting; phagocyting antigens directly. They are \gls{APC} (since they display class II \acrshort{MHC} complexes). It is thought they act as \gls{APC} so that experienced T cells can be restimulated while traveling the blood stream.},
}
\newglossaryentry{dendritic}{
name={dendritic cell},
description={are ``sentinel'' cells which take up positions beneath the barriers of epithelial cells. They are starfished-shape and so can capture opsonized antigens. \emph{See:} section \ref{dendritic}.},
}
\newglossaryentry{bcell}{
name={B cell},
description={attack free antigens that are detected by the adaptive system by the production of antibody molecules into the blood stream. This is called the humoral response. \emph{See:} section \ref{bcell}.},
}
\newglossaryentry{thcell}{
name={helper T cell},
description={act as a gateway between dendritic cells and B cells, as a decision maker, sniffing the non-selfness of the presented antigen. Remember B cells are only activated after confirmation by a helper T cell, for most antigens (T-cell dependent antigens).\newline Aka: T\textsubscript{H}; CD4\textsuperscript{+} T cell. \emph{See:} section \ref{thcell}.},
}
\newglossaryentry{tccell}{
name={killer T cell},
description={activate apoptosis (the self-destruction mechanism) of cells if it binds to class I MHC molecules, which are located within the interior of the cell.\newline Aka: cytotoxic T cell; T\textsubscript{C}; CTL; CD8\textsuperscript{+} T cell. \emph{See:} section \ref{tccell}.},
}
\newglossaryentry{NK}{
name={natural killer},
description={are corollaries to killer T cells. It destroys cells that fail to produce class I MHC molecules; those  may be ``stressed'' cells, or may be hiding a virus. They kill indiscriminately, and are therefore categorized as part of the innate system. \emph{See:} section \ref{NK}},
}
\newglossaryentry{HIV}{
name={HIV},
description={refers to the human retrovirus causing AIDS. A retrovirus is a lifeless molecular envelope of RNA and several enzymes to convert and merge viral RNA into cellular DNA. Life refers to any molecule that contains instructions responsible for its self-replication, which retroviruses do not contain --- they require a host cell and is why it is considered lifeless. \acrshort{HIVa} infects cells displaying CD4 proteins on the surface --- primarly, \glspl{thcell}. Two HIV virus species exist, though this (and most) work concerns HIV-1 which is the variant of \acrshort{HIVa} widespread outside of Africa. The virus is much smaller than \glspl{white blood cell} --- it is pictured in green in the image. \emph{See:} section \ref{hiv}.},
}


\newglossaryentry{lymphocyte}{
name={lymphocyte},
description={the family of cells: T cell, B cell and Natural Killer. These cells are named lymphocytes because they are the main cells found in the \gls{lymph node}. \emph{See:} section \ref{lymphocyte}.},
}
\newglossaryentry{lymph node}{
name={lymph node},
description={is an oval-shaped organ widely distributed throughout the body. \emph{See:} section \ref{lymph node}.},
}



%% BIOLOGY COMMON

\newglossaryentry{pathogen}{
name={pathogen},
description={synonymous of infectious agent (colloquially known as \emph{germ}); any microorganism, such as a virus, bacterium, prion, fungus or protozoan, that causes disease in its host.},
}
\newglossaryentry{white blood cell}{
name={white blood cell},
description={synonymous of immune cells; the agents responsible for our immune defenses.\glsadd{red blood cell}},
}
\newglossaryentry{red blood cell}{
name={red blood cell},
description={blood cells carrying oxygen.},
}

\newglossaryentry{specificity}{
name={specificity},
description={molecular specificity refers to the complementary needed for two molecules to bind. \emph{See:} section \ref{specificity}},
plural={specificities}
}
\newglossaryentry{affinity}{
name={affinity},
description={\emph{See:} \gls{specificity}},
plural={affinities}
}

\newglossaryentry{apoptsis}{
name={apoptsis},
description={programmed cell death mechanism, used to dispose of damaged or unneeded cells. \emph{Related:} \gls{lysis}},
plural={apoptsis}
}
\newglossaryentry{lysis}{
name={lysis},
description={cell death by bursting, often by a virus or other means by which the integrity of the cellular membrane is compromised. \emph{Related:} \gls{apoptsis}},
plural={lysis}
}



\newglossaryentry{enzyme}{
name={enzyme},
description={are catalysts that convert molecules (subtracts) into other molecules (products); for instance, the \gls{reverse transcriptase} that converts viral RNA into cellular DNA.},
}
\newglossaryentry{reverse transcriptase}{
name={reverse transcriptase},
description={is an \gls{enzyme} that converts a RNA template into complementary DNA; transported and used by the \gls{HIV} molecule.},
}


%% BIOLOGY LESS COMMON

\newglossaryentry{point mutation}{
name={point mutation},
description={A type of mutation that causes the replacement of a single base of nucleotide, such as DNA or RNA. Also known as single-base-pair mutation},
}




%% RECEPTORS

\newacronym{BCR}{BCR}{B Cell Receptor}
\newacronym{TCR}{TCR}{T Cell Receptor}

\newacronym{ODE}{ODE}{ordinary differential equation}
\newacronym{PDE}{PDE}{partial differential equation}
\newacronym{SDE}{SDE}{stochastic differential equation}
\newacronym{CTMC}{CTMC}{continuous time markov chain}
\newacronym[\glslongpluralkey={cellular automata}]{CA}{CA}{cellular automaton}
\newacronym{ABM}{ABM}{agent-based model}

\newacronym{HIVa}{HIV}{human immunodeficiency virus}
